Bioconductor / GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.
http://bioconductor.github.io/GenomicDataCommons/
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Error: lexical error: invalid char in json text. #54

Closed bioinfo-dirty-jobs closed 6 years ago

bioinfo-dirty-jobs commented 6 years ago

Here the error:


                               type == 'gene_expression' &
+                                analysis.workflow_type == 'HTSeq - Counts')
> manifest_df = qfiles %>% manifest()
Error: lexical error: invalid char in json text.
                                       <?xml version="1.0" encoding="U
                     (right here) ------^
sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_2.2.1            knitr_1.20               GenomicDataCommons_1.2.0
[4] magrittr_1.5            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17           pillar_1.2.3           compiler_3.4.4        
 [4] BiocInstaller_1.28.0   GenomeInfoDb_1.14.0    plyr_1.8.4            
 [7] XVector_0.18.0         bitops_1.0-6           tools_3.4.4           
[10] zlibbioc_1.24.0        jsonlite_1.5           tibble_1.4.2          
[13] gtable_0.2.0           pkgconfig_2.0.1        rlang_0.2.0           
[16] rstudioapi_0.7         curl_3.2               yaml_2.1.19           
[19] parallel_3.4.4         GenomeInfoDbData_1.0.0 httr_1.3.1            
[22] xml2_1.2.0             S4Vectors_0.16.0       IRanges_2.12.0        
[25] hms_0.4.2              stats4_3.4.4           grid_3.4.4            
[28] data.table_1.11.4      R6_2.2.2               readr_1.1.1           
[31] scales_0.5.0           BiocGenerics_0.24.0    GenomicRanges_1.30.3  
[34] colorspace_1.3-2       labeling_0.3           utf8_1.1.4            
[37] RCurl_1.95-4.10        lazyeval_0.2.1         munsell_0.4.3         
[40] crayon_1.3.4 
seandavi commented 6 years ago

Upgrading to version 1.4.1 (the current release version) should fix the issue. A change on the NCI GDC server causes this error, so an upgrade is required. Sorry about the inconvenience.